New tutorial about genome annotation, comparative genomics and visualization

CONTRIBUTORS.yaml

@@ -2790,6 +2790,18 @@ Sofokli5:
     orcid: 0000-0002-4833-4726
     joined: 2022-05
 
+soniacasillas:
+    name: Sònia Casillas
+    email: sonia.casillas@uab.cat
+    orcid: 0000-0001-8191-0062
+    joined: 2025-11
+    contact_for_training: true
+    location:
+      country: ES
+      lat: 41.64
+      lon: 2.41
+    bluesky: scasillasv.bsky.social
+
 sophia120199:
     name: Sophia Hampe
     joined: 2023-04

topics/genome-annotation/tutorials/genome-annotation-comparison-visualization/data-library.yaml

@@ -0,0 +1,64 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Genome Annotation
+  description: In this tutorial, you will perform a complete workflow for fungal genome annotation, comparative genomics, and visualization. Starting from raw Mucor mucedo genomic and RNA-seq data, you will run Funannotate to generate structural and functional annotations. The predicted proteome is then compared with complete proteomes from related Mucor species and Saccharomyces cerevisiae using OrthoFinder to identify orthogroups and assess evolutionary relationships. Finally, the annotated genome and comparative results are explored and visualized using JBrowse2 for interactive genome browsing and Circos to display synteny and genomic relationships.
+  items:
+  - name: Genome annotation (Funannotate), comparison (OrthoFinder) and visualization
+      (JBrowse2 & Circos) [Galaxy Training Material]
+    items:
+    - name: 'DOI: 10.5281/zenodo.17612216'
+      description: latest
+      items:
+      - url: https://zenodo.org/records/17612216/files/genome_masked.fasta
+        src: url
+        ext: fasta
+        info: https://zenodo.org/records/17612216
+      - url: https://zenodo.org/records/17612216/files/rnaseq_R1.fq.gz
+        src: url
+        ext: fastqsanger.gz
+        info: https://zenodo.org/records/17612216
+      - url: https://zenodo.org/records/17612216/files/rnaseq_R2.fq.gz
+        src: url
+        ext: fastqsanger.gz
+        info: https://zenodo.org/records/17612216
+      - url: https://zenodo.org/records/17612216/files/SwissProt_subset.fasta
+        src: url
+        ext: fasta
+        info: https://zenodo.org/records/17612216
+      - url: https://zenodo.org/records/17612216/files/UP000002311_559292.fasta.gz
+        src: url
+        ext: fasta.gz
+        info: https://zenodo.org/records/17612216
+      - url: https://zenodo.org/records/17612216/files/UP000014254_1220926.fasta.gz
+        src: url
+        ext: fasta.gz
+        info: https://zenodo.org/records/17612216
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+        src: url
+        ext: fasta.gz
+        info: https://zenodo.org/records/17612216
+      - url: https://zenodo.org/records/17612216/files/UP000077051_747725.fasta.gz
+        src: url
+        ext: fasta.gz
+        info: https://zenodo.org/records/17612216
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+        src: url
+        ext: fasta.gz
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+        src: url
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+        info: https://zenodo.org/records/17612216
+      - url: https://zenodo.org/records/17612216/files/UP001304243_708070.fasta.gz
+        src: url
+        ext: fasta.gz
+        info: https://zenodo.org/records/17612216
+      - url: https://zenodo.org/records/17612216/files/UP001473302_439312.fasta.gz
+        src: url
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+        info: https://zenodo.org/records/17612216

topics/genome-annotation/tutorials/genome-annotation-comparison-visualization/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/genome-annotation/tutorials/genome-annotation-comparison-visualization/tutorial.bib

@@ -0,0 +1,48 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Wang2023,
+  title = {Divergent Evolution of Early Terrestrial Fungi Reveals the Evolution of Mucormycosis Pathogenicity Factors},
+  volume = {15},
+  ISSN = {1759-6653},
+  url = {http://dx.doi.org/10.1093/gbe/evad046},
+  DOI = {10.1093/gbe/evad046},
+  number = {4},
+  journal = {Genome Biology and Evolution},
+  publisher = {Oxford University Press (OUP)},
+  author = {Wang,  Yan and Chang,  Ying and Ortañez,  Jericho and Peña,  Jesús F and Carter-House,  Derreck and Reynolds,  Nicole K and Smith,  Matthew E and Benny,  Gerald and Mondo,  Stephen J and Salamov,  Asaf and Lipzen,  Anna and Pangilinan,  Jasmyn and Guo,  Jie and LaButti,  Kurt and Andreopolous,  William and Tritt,  Andrew and Keymanesh,  Keykhosrow and Yan,  Mi and Barry,  Kerrie and Grigoriev,  Igor V and Spatafora,  Joseph W and Stajich,  Jason E},
+  editor = {Ma,  Li-Jun},
+  year = {2023},
+  month = mar 
+}
+
+@misc{https://doi.org/10.5281/zenodo.7867921,
+  doi = {10.5281/ZENODO.7867921},
+  url = {https://zenodo.org/record/7867921},
+  author = {Bretaudeau,  Anthony and Cormier,  Alexandre and Robin,  Stéphanie and Corre,  Erwan and Leroi,  Laura},
+  keywords = {training,  galaxy,  genome annotation},
+  title = {Training data for 'Genome annotation with Funannotate' tutorial (Galaxy Training Material)},
+  publisher = {Zenodo},
+  year = {2021},
+  copyright = {Creative Commons Attribution 4.0 International}
+}
+
+@online{gtn-website,
+  author = {GTN community},
+  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
+  url = {https://training.galaxyproject.org},
+  urldate = {2021-03-24}
+}